A Choice Encounter
by ArcanaMajorEmpress
Summary: Kara Zor-El is selfless. She is brave. She is strong, and she is bold. But there are those out there who wish to cause our hero harm. And some will go to any lengths to achieve it.
1. Knives and Nails

Kara Zor-El was not the kind of hero to ignore where help was needed.

Granted, she was late for work, and the wrath of her boss was enough to cause even the girl of steel to shudder. But CatCo would have to wait. Right now, Supergirl had something much more important on her plate.

"Please, that's all I have - Wait! Let me go! Please don't hurt me!" Kara beelined towards the shouts, spotting a young man, maybe in his late teens, struggling against the hold of what appeared to be a couple of muggers, before they noticed her. The two dropped the kid and ran into the alley, rightfully in fear of the now furious Kryptonian.

She landed, righting the still terrified teen as he stumbled. "Are you alright? Were you hurt at all?" He shook his head and stepped back.

"..thank you!" He whispered, nodding, and then jogged off.

"Hey, wait! Don't you want your things back?" He was already gone. Odd.

She spun around, prepared to face the criminals. They couldn't have gotten too far. She sprinted into the shadows, only to catch a black BMW rolling away, a screeching turn emitting as it drove off. She flew after it, employing her x-ray vision to see the figures inside. Three people; one driver and the two aggressors. She increased her speed, rolling and touching down inches in front of the vehicle as it came to a shrieking halt. But not before they made the unfortunate choice of trying to mow her down.

The sound of metal whining as it crushed itself against the heroine, effortlessly fixed in place, could be heard for blocks. The next mistake of the criminals was to exit the car and attempt to run. "Honestly, you thought that was going to work?" She flipped the driver, securing him to the nearest flickering streetlamp. Skidding in front of the remaining two, she grabbed their arms and wrapped them to the same lamp with their own jackets. "That'll do until I get the police over here. I hope you three learn your lesson about crime in National City, friends."

Kara stepped to the totaled car, pulling off it's hatch to search the boot for stolen property. Nothing there. She spun around. "Which one of you has the-"

She was speaking to no one. The only evidence of the crooks was a few fresh scratches left on the peeling paint of the light pole. She scanned the area, finding nothing. Wait, there was a person over... "You can't hide from me, you know!"

"Thank you for your cooperation, Agent Danvers. We'll be taking it from here." Her sister's terrified gasp was the last thing she heard before she blacked out.

* * *

"Kara Danvers..." Step-tap. Step-tap. Step-tap. "Kara.. Zor-El..." Tap-step. Tap-step. Tap-step.

A light seared the inside of her eyelids, but she could not lift them.

" _Su_ - _per_ - _girl_." The voice was steady, but taunting. It hurt her ears.

A hand, a set of sharp nails, clutching her arm, bringing her wrist up to examine.

"I'm sure you're aware that you and your little. _Friends_. Back at base have been causing me quite a bit of trouble as of late, hmm?" Heels continued to clack, pacing behind Kara's pounding head.

The voice became shrill. "Open your eyes, girl. We have places to infiltrate, people to find, and things to achieve."  
The voice let out an exasperated sigh. "I don't have all day, you know."

Her own voice was raspy and her mouth dry. "...who?"

"An elegant question, my dear hero. Just follow orders, try not to make too much fuss, and all of your questions will be answered in due time.." The footsteps receded and a door groaned shut, leaving nothing but the uncomfortable light and a feeling of dread ebbing away at her aching mind.

* * *

 **That's all I've got right now. So, how do you like my first Supergirl fic? Please tell me what you liked and didn't, it would mean a lot!**

 **Also, guess who got "Clark K./Superman" added to the character list? That's right, this bish! (oh lord what have i done now everybody is going to start making incest fics aren't they)**


	2. Redirection

She groaned, stretching. Her body was sore, and she could feel bruises formed on her back and arms. Alex's eyes flickered, before she opened them slowly to reveal her uncomfortable choice of bedding. _Had she passed out? Had she been drinking? No... she never got drunk..._

"Kara."

Agent Danvers struggled to sit up, gasping as the memories flooded back. _A call. A phone call, and a voice claiming to be from the DEO. Instructions..._ She rubbed her head where it still hurt. _A conversation about her sister's whereabouts... she called her Kara. She called her Supergirl. And she..._

 _Kara._

Shaking as she rose, she took in her surroundings. They must have dumped her when they were done interrogating her. But wouldn't that be a security risk? Alex reached for her phone, only to grab air. _Shit_.

"You wont be needing your phone, where you're going." She started and spun around, fists raised. "Glad to see you finally woke up. They weren't kidding when they said that they'd misplaced you. But it still serves as a nice tracker to find you." The figure's eyes crinkled in evident smugness as they flipped Alex's phone in their hands. Shorter and slim, they were clad in a dark grey uniform and a matching mask and hood. A gun was strapped to their side, and a hand pointedly resting over it.

"What did you do with Kara? Where is she?" She took a step towards them, attempting to appear more powerful than she currently felt.

They let out a chuckle, pocketing the phone. "Still, you care more about your sister than your own immediate safety. Just like you to do, really. It's honorable; that selflessness has always impressed me."

"Who-" The figure's eyes widened and they made to cover Alex's mouth. "-mrgmm -" She swatted the hand away. "Tell me what you've done with my sister!"

"Not so loud, damn it!" The now-silhouette of a person whispered. They cast a cursory glance around before grabbing Alex's hand and pulling her into the shadow and out of the light of the approaching motorcycle.

They stood like that until the bike couldn't be seen or heard, before she was led back into the street. "Do I know you? Why haven't you hurt me - you do work with them, don't you?" She asked, voice confused and glare beginning to falter.

Shaking their head and pulling down the mask they let out a tisk. "That's what they think."

"Ah-Maggie?!" She took a step back, unable to believe her own eyes. "I haven't seen you in months! I'd thought that you'd left, I.." Agent Sawyer answered with a shake of her head.

"Undercover. I'd hoped I wouldn't have to tell you so soon, but as we can see, they've gone ahead with their plans a little early."

"What have they done with Supergirl, Maggie?"

"Well, I wish that I could tell you, but that's what I'm here to find out. That, and to make sure you're safe and not alone on the streets at night. Are you hurt at all?" She lifted Alex's hand, squinting in the dark at her scrapes.

"I'll... I'll be alright. I'm just a little beat up, I guess."

"So long as you don't have a concussion, then, I suppose." Maggie paused. "Also, you really ought to be more careful about referring to Kara consistently."

"I - _frick_."

"Don't you worry. I keep a secret." Maggie smirked and brought out a hair-tie. "Now then. Let's save Supergirl."

* * *

Cat Grant was the most powerful CEO in all of National City. And if she didn't have an ego to maintain, she might comment on Maxwell Lord's own opinion, but she just didn't have the time to care.

Certainly not with her personal assistant missing. Again.

This last year Kira had gone from a perfect attendance to periodic lateness and absences. It was getting on Cat's nerves. Especially as she stood, in the middle of her floor, purse in one hand, and no latte in the other. "KIERRA. Where is she?" She turned to stare at the IT gremlin, Toyman jr. or whatever his name was, but he was nowhere to be found. At least Superpal would have an explanation for her. One of them always conveniently did.

"Jimmy. Where's my assistant?"

"It's Ja.." Cat raised an eyebrow. James cleared his throat. "Right, _Kara_ , is, well..." He glanced at the TV, searching for anything to use as an excuse. He hadn't expected Kara to be missing today. "There was a pile-up on the corner when she was retrieving your latte, Ms. Grant, and it's causing complications. She'll be here as soon as possible, I'm sure." He cashed in a reassuring smile, just for good measure.

Without so much as a peek towards the muted screens, Cat didn't miss a beat. "That wreck happened ten minutes ago, and Kerah is coming up on thirty minutes late. I would advise both you and your little computer friend to work on your excuses, since you seem to use them so much."

And with that, she pivoted a turn and marched to her office, sitting down with a huff and an unsatisfied expression. She spun her chair around, only to be faced with a series of new headlines streaming from the monitors in front of her.

SUPERGIRL MISSING ?

NO SIGN OF HERO AS TROUBLE ENSUES IN NATIONAL CITY

GIRL OF STEEL MIA

Well, that was odd.

* * *

 **Two chapters in one day! Sorry for them being so short. And I feel like this one is really sub-par. Ah well. Thank you for all of your support! The only time I've ever gotten so many emails in an hour was when I presented my current events issue in ApEng. *shudders* And those were not so nice of messages.**


	3. Bikes and Hounds

**Pronounced "loop," a loupe refers to those magnifying eyeglasses that a dentist might wear.**

* * *

"Maggie?"

"Hm?"

"When I was knocked out and you found me, why did you just let me lay there until I woke up?" Her voice still held some strain to it, but her tone was not accusatory.

She gave a tight-lipped smile, although Alex couldn't see it from behind Maggie's back, as they rode her motorbike past city lights and boulevards, slowing down only as they approached what imitated a vacant lot. "Oh, good. No drug lords."

Alex waited patiently as Maggie stopped the bike and came to a halt near the center of the shrouded area, before she turned around to face the DEO agent, who was waiting for her answer.

"I didn't know how badly you were hurt. I didn't want to risk causing more injury by moving you." She parked the bike, leaving the keys in the ignition and turning back around. "That, and I didn't have anywhere to put you. I'm lucky that you were able to walk."

Alex looked her in the eyes for a moment, then slowly nodded, unblinking in the shallow air around them.

Maggie tensed. _That's not really what you meant to ask_. The words were left unspoken, but the communication still occurred.

"I should call Kara's friends. Ask them what they know."

The agent slid off of the seat and onto the cracked concrete, weathered and run with weeds by lack of care. Her phone screen gleamed, illuminated only by the headlight and a yellowed lamp overhead.

She selected a contact, scrolling down to the 'call' option and sliding the cold phone against her ear. After some minutes, she began to pace, impatient and anxious as to why it was taking him so long. After the fourth antagonizing ring, she stomped her foot and let out a huff of exasperation, eyes to the sky, and turned back to her teammate as she was dumped in voicemail. "Winn's not picking up."

"I can see that. But that's the fifth time now that you've called the guy, Alex. He's not going to answer. Is there anyone else to call? Some one who could help us find Kara?"

She straightened from her slouch and gave a nod, again sliding through her list. "Maybe. Have you met James?"

* * *

Breath in. _Shudder,_ and breath out. And _shudder,_ and inhale, and _shudder,_ exhale. Like a constant tempo as she drew and released each breath, her lungs kept a steady flow, totaling the time as it passed. A perpetual symphony, respiration. Reliable, unfaltering _air_.

She was lucky Earth harbored it at all, even if more than a tad contaminated.

, and _gasp_ -

The light wasn't what stung when she next opened her eyes. Staring skyward and laid out on cold steel, her flinching gaze was met only by a masked face and the intense glare of the loupes that obscured it.

"Madam, the patient is reacting positively to the formula. We can infer consciousness."

The next voice was no higher a pitch, albeit not low in itself.

"About time, Wilder." The familiar clicking announced itself once again, drawing in as the masked doctor drew back. It paused, near. "Give us the room."

The first voice's response was a mistake on his part. "Madam, I apologize, but the patient isn't necessarily stabl-"

" _Did I **ask**?_ " She would have recoiled, had she the control of her body. Or of feeling, for that matter. Kara couldn't quite recall where she had left her feet.

"No, Madam. I apologize." They waited until the man had scurried out, in the manner of a scolded hound - faithful but tail tucked, before the heels once again her way clicked.

Blurred and clouded by Kara's sore eyes, the woman's face manifested itself among the greys and blues of the room. "I have a gift for you, Miss Zor-El."

* * *

 **The reason Winn hasn't been present isn't because I don't like him, I swear. Just be patient, unlike me!**

 **Chappy Channukah and happy assorted Kislev and december holidays (Christmas is today, right?), and here's a mini chapter because I pack everything into tiny bite sizes, allowing for everything to happen before I have to change scenes and then run out of things to do before a chapter break. Gotta love having a linguistics-wired brain that isn't even good at writing but can complain in bold for hours. (: hmu if you can relate I must know.**


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